Hillary Clinton’s relationship with the press is notoriously contentious, but on Thursday the situation rose above the usual low-grade sniping and resentment. In a nearly 2,000 word letter posted on Clinton’s website, communications director Jennifer Palmieri blasted the New York Times for “egregious” errors and an “apparent abandonment of standard journalistic practices.” So, why did the campaign feel the need to “officially register” its “grave concern” about the paper’s reporting? It all started last week, when a push alert went out to Times readers’ phones: “A criminal inquiry is being sought over Hillary Clinton’s email use.” Over the next few days, the Clinton team and various government officials chipped away at the report, and the Times was forced to clarify that Clinton herself is not the target of a potential federal criminal investigation, and in fact the referral was not“criminal.”

The timing of the letter’s release seems a bit strange, as the Times has already dissected its reporting and partially admitted that it botched the report at the start of the week. Clinton press secretary Brian Fallon told CNNMoney that the campaign sent the letter to Times executive editor Dean Baquet on Tuesday, but the paper refused to publish it. Thus, though the controversy was already dying down, the Clinton team opted to hit back at the paper. In case you missed all the after-hours twists and turns that led to the top Democratic presidential candidate calling out the nation’s leading paper, here’s arecap.

Times posts Clinton email report, quietly changes it.Late on Thursday, June 23, the paper posted a story titled “Criminal Inquiry Sought in Hillary Clinton’s Use of Email.” It began with thelede:

Two inspectors general have asked the Justice Department to open a criminal investigation into whether Hillary Rodham Clinton mishandled sensitive government information on a private email account she used as secretary of state, senior government officials saidThursday.

About an hour later, the headline was changed to “Criminal Inquiry Is Sought in Clinton Email Account” (along with the URL), and the lede was rewritten to put some distance between Clinton and the potentially criminalbehavior.

Two inspectors general have asked the Justice Department to open a criminal investigation into whether sensitive government information was mishandled in connection with the personal email account Hillary Rodham Clinton used as secretary of state, senior government officials saidThursday.

At 3 a.m., Clinton spokesman Nick Merrill released the followingstatement:

Politico’s Dylan Byers noted that early on Friday morning there was still no note from the Times indicating that the article had been changed. He said one of the story’s reporters, Michael Schmidt, explained, “It was a response to complaints we received from the Clinton camp that we thought were reasonable, and we madethem.”

Representative Elijah Cummings denies there was a request for a criminal investigation.On Friday morning, Representative Elijah Cummings, the top Democrat on the House Select Committee on Benghazi, issued a statement rebutting the report that there had been a request for a federal criminal investigation into Clinton’semail:

I spoke personally to the State Department Inspector General on Thursday, and he said he never asked the Justice Department to launch a criminal investigation of Secretary Clinton’s email usage. Instead, he told me the Intelligence Community IG notified the Justice Department and Congress that they identified classified information in a few emails that were part of the FOIA review, and that none of those emails had been previously marked asclassified.

In other words, the Times identified the wrong inspectors general, and the Intelligence Community IG just let the Justice Department know that some of the emails being reviewed under the Freedom of Information Act should have been marked classified and withheld from the public — though they were not marked classified when they were in Clinton’spossession.

The Justice Department confirms that there was no criminal referral.A Justice Department official said they were only asked to look into how the release of Clinton’s emails is being handled. “The Department has received a referral related to the potential compromise of classified information. It is not a criminal referral,” the official toldPolitico.

The Times says the article does not require a correction.In an email to the Washington Post’s Erik Wemple, New York Times spokeswoman Eileen Murphy said, “As often happens, editors continued to revise this story after initial publication to make it as clear and precise as possible. There was no factual error, so there was no reason for acorrection.”

Clinton addresses the controversy.During a speech on the economy in New York, Clinton criticized the Times report, joking, “Maybe the heat is getting to everybody.” She added, “I have released 55,000 pages of emails. I have said repeatedly that I will answer questions before the House committee. We are all accountable to the American people to get the facts right and I will do mypart.”

The Times issues a correction.Shortly after 2 p.m. on Friday, the papersaid:

An earlier version of this article and an earlier headline, using information from senior government officials, misstated the nature of the referral to the Justice Department regarding Hillary Clinton’s personal email account while she was secretary of state. The referral addressed the potential compromise of classified information in connection with that personal email account. It did not specifically request an investigation into Mrs.Clinton.

David Brock calls for a review of the paper’s reporting.The Media Matters for America chairman issued an open letter calling on the Times to “address the situation by commissioning a review that will explore the process of reporting and editing at The New York Times that has allowed flawed, fact-free reporting on so-called scandals involving Hillary Clinton and report back toreaders.”

David Brock is a partisan. It is not surprising that he is unhappy with some of our aggressive coverage of important political figures. We are proud of that coverage and obviously disagree with hisopinion.

Newsweek’s Kurt Eichenwald shreds the entire Times report.In an article posted on the night of Friday, June 24, Eichenwald, a former Times reporter who has previously criticized the paper’s reporting on Clinton’s private email account, alleges that “almost every paragraph at the top of the story is wrong, misleading or fundamentally deceptive.” Citing Congressman Cummings’s claim that the Justice Department, which issues regulations on FOIA requests, was simply notified that some emails were not properly marked “classified,” Eichenwaldasked:

So had the Times mixed up a criminal referral—a major news event—with a notification to the department responsible for overseeing FOIA errors that might affect some documents’ release? It’s impossible to tell, because the Times story—complete with its lack of identification of any possible criminal activity—continues to mention a criminalreferral.

He went on to explain that he had reviewed documents from the inspectors general and found inaccuracies in the Times report that went far beyond whether there was criminal inquiry (he acknowledged that there is a small chance the Times had different memos, with incredibly similar dates andquotes):

Here are the words that were left out: Freedom of Information Act. At no point in the story does the Times mention what this memo—and the other it cited—was really all about: that the officials at the Freedom of Information office in the State Department and intelligence agencies, which were reviewing emails for release, had discovered emails that may not have been designated with the correct classification. For anyone who has dealt with the FOIA and government agencies, this is something that happens all the time in every administration…

The problem is, it is not as if the real purpose of this memo was hard to discern. Here is the subject heading: “Potential Issues Identified by the Office of the Inspector General of the Intelligence Community Concerning the Department of State’s Process for the Review of Former Secretary Clinton’s Emails under the Freedom of Information Act(ESP-15-05)”

Get it? This is about the process being used by FOIA officials in reviewing former Secretary Clinton. And former government officials have nothing to do with how FOIA officials deal with requests for documentation. To jump from this fact to a conclusion that, somehow, someone thinks there is a criminal case against Clinton (the original story) requires a level of recklessness that borders on, well, criminalbehavior.

In terms of journalism, this is terrible. That the Times article never discloses this is about an after-the-fact review of Clinton’s emails conducted long after she left the State Department is simply inexcusable. That this all comes from a concern about the accidental release of classified information—a fact that goes unmentioned—is even worse. In other words, the Times has twisted and turned in a way that makes this story seem like something it most decidedly is not. This is no Clinton scandal. It is no scandal at all. It is about current bureaucratic processes, probably the biggest snooze-fest in all ofjournalism.

The Times removes the word criminal from the original story.On Saturday morning, the paper revised the original report again, changing the headline to “Inquiry Sought in Hillary Clinton’s Use of Email.” The word criminal was also removed from the lede, and a second correction wasadded:

An article in some editions on Friday about a request to the Justice Department for an investigation regarding Hillary Clinton’s personal email account while she was secretary of state referred incorrectly, using information from senior government officials, to the request. It was a “security referral,” pertaining to possible mishandling of classified information, officials said, not a “criminalreferral.”

According to Politico’s Dylan Byers, multiple sources said the Justice Department initially told the Times and other news organizations that the referral was “criminal.” On Friday afternoon, TheWall Street Journalreported that an internal government review found Clinton sent at least four emails that contained classified information through her personal account, and the matter had been referred to the Justice Department. The paper noted, “Initially, a Justice Department official said Friday morning the investigation was criminal in nature, but the department reversed course hours later withoutexplanation.”

The Times defended itself further in its own report on the four emails that “contained government secrets,” which appeared on the front page of Saturday’spaper:

The discovery of the four emails prompted [I. Charles McCullough III, inspector general for the intelligence community] to refer the matter to F.B.I. counterintelligence agents, who investigate crimes related to the mishandling of classified information. On Thursday night and again Friday morning, the Justice Department referred to the matter as a “criminal referral,” but later Friday dropped the word “criminal.” The inspectors general said late Friday that it was a “security referral” intended to alert authorities that “classified information may exist on at least one private server and thumb drive that are not in the government’s possession.” Irrespective of the terminology, the referral raises the possibility of a Justice Department investigation into Mrs. Clinton’s emails as she campaigns for president. Polls show she is the front-runner for the Democratic nomination by a wide margin. Mishandling classified information is a crime. Justice Department officials said no decision had been made about whether to open a criminalinvestigation.

The Times public editor tackles the story.Margaret Sullivan posted her assessment on Monday, calling it a “messy and a regrettable chapter.” Editor Matt Purdy and reporters Matt Apuzzo and Michael S. Schmidt gave her more information on how the report cametogether:

The story developed quickly on Thursday afternoon and evening, after tips from various sources, including on Capitol Hill. The reporters had what Mr. Purdy described as “multiple, reliable, highly placed sources,” including some “in law enforcement.” I think we can safely read that as the JusticeDepartment.

The sources said not only was there indeed a referral but also that it was directed at Mrs. Clinton herself, and that it was a criminal referral. And that’s how The Times wrote itinitially.

“We got it wrong because our very good sources had it wrong,” Mr. Purdy told me. “That’s an explanation, not an excuse. We have an obligation to get facts right and we work very hard to dothat.”

Executive editor Dean Baquet acknowledged that the Times should have been more transparent about thecorrections:

“We should have explained to our readers right away what happened here, as soon as we knew it,” he said. That could have been in an editor’s note or in a story, or in some other form, hesaid.

“The readers of The New York Times got whipsawed,” by all the conflicting reports and criticism, hesaid.

He agreed, as Mr. Purdy did, that special care has to come with the use of anonymous sources, but he believes that the errors here “may have been unavoidable.” And Mr. Purdy said that he thought The Times probably took too long to append a correction in the firstinstance.

But, Mr. Baquet said, he does not fault the reporters or editors directlyinvolved.

“You had the government confirming that it was a criminal referral,” Mr. Baquet said. “I’m not sure what they could have done differently onthat.”

Sullivan said she thinks the paper needs to consider how it uses anonymous sources and be more cautious in the future, even if it means missing a scoop. “I’ll summarize my prescription in four words: Less speed. More transparency,” shewrote.

The Times releases an editor’s note on Clinton email coverage. The note defended the original story, saying it was “based on multiple high-level government sources,” but it also acknowledged that the corrections should have been notedimmediately:

The original article, however, was not altered online until Saturday morning to take account of the change in description of the referral from “criminal” to “security.” Editors should have added a correction sooner to note thatchange.

The Clinton campaign posts an open letter to the Times. Palmieri began by acknowledging that several Times editors have already commented on the erroneous report, but said, “We remain perplexed by the Times’ slowness to acknowledge its errors after the fact, and some of the shaky justifications that Times’ editors have made.” She went on to allege that the story was “reportedly hastily” and the campaign wasn’t given enough time torespond:

It was not even mentioned by your reporter when our campaign was first contacted late Thursday afternoon. Initially, it was stated as reporting only on a memo – provided to Congress by the Inspectors General from the State Department and Intelligence Community – that raised the possibility of classified material traversing Secretary Clinton’s email system. This memo — which was subsequently released publicly — did not reference a criminal referral at all. It was not until late Thursday night – at 8:36 pm – that your paper hurriedly followed up with our staff to explain that it had received a separate tip that the Inspectors General had additionally made a criminal referral to the Justice Department concerning Clinton’s email use. Our staff indicated that we had no knowledge of any such referral – understandably, of course, since none actually existed – and further indicated that, for a variety of reasons, the reporter’s allegation seemed implausible. Our campaign declined any immediate comment, but asked for additional time to attempt to investigate the allegation raised. In response, it was indicated that the campaign “had time,” suggesting the publication of the report was notimminent.

Despite the late hour, our campaign quickly conferred and confirmed that we had no knowledge whatsoever of any criminal referral involving the Secretary. At 10:36 pm, our staff attempted to reach your reporters on the phone to reiterate this fact and ensure the paper would not be going forward with any such report. There was no answer. At 10:54 pm, our staff again attempted calling. Again, no answer. Minutes later, we received a call back. We sought to confirm that no story was imminent and were shocked at the reply: the story had just published on the Times’website.

Next Palmieri claimed the Times “relied on questionable sourcing,” though the paper said it received the incorrect information from the JusticeDepartment:

Times’ editors have attempted to explain these errors by claiming the fault for the misreporting resided with a Justice Department official whom other news outlets cited as confirming the Times’ report after the fact. This suggestion does not add up. It is our understanding that this Justice Department official was not the original source of the Times’ tip. Moreover, notwithstanding the official’s inaccurate characterization of the referral as criminal in nature, this official does not appear to have told the Times that Mrs. Clinton was the target of that referral, as the paper falsely reported in its originalstory.

This raises the question of what other sources the Times may have relied on for its initial report. It clearly was not either of the referring officials – that is, the Inspectors General of either the State Department or intelligence agencies – since the Times’ sources apparently lacked firsthand knowledge of the referral documents. It also seems unlikely the source could have been anyone affiliated with those offices, as it defies logic that anyone so closely involved could have so severely garbled the description of thereferral.

In case you could not decipher this blind item, here’s a hint from columnist MichaelCohen:

This entire Clinton letter to the NYT is one massive subtweet: "why did you rely on Trey Gowdy as a source" https://t.co/xUlqOVH49P

After further questioning why it took the Times so long to issue a correction, Palmieri said the Clinton team hopes they can still befriends:

In closing, I wish to emphasize our genuine wish to have a constructive relationship with The New York Times. But we also are extremely troubled by the events that went into this erroneous report, and will be looking forward to discussing our concerns related to this incident so we can have confidence that it is not repeated in thefuture.

When asked for comment, a Times spokeswoman told CNNMoney, “Our editor’s note and the public editor fully addressed the issues related to this story and we don’t plan to commentfurther.”